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Liu J, Kandel SE, Lampe JN, Scott EE. Human cytochrome P450 3A7 binding four copies of its native substrate dehydroepiandrosterone 3-sulfate. J Biol Chem 2023; 299:104993. [PMID: 37392852 PMCID: PMC10388207 DOI: 10.1016/j.jbc.2023.104993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Human fetal cytochrome P450 3A7 (CYP3A7) is involved in both xenobiotic metabolism and the estriol biosynthetic pathway. Although much is understood about cytochrome P450 3A4 and its role in adult drug metabolism, CYP3A7 is poorly characterized in terms of its interactions with both categories of substrates. Herein, a crystallizable mutated form of CYP3A7 was saturated with its primary endogenous substrate dehydroepiandrosterone 3-sulfate (DHEA-S) to yield a 2.6 Å X-ray structure revealing the unexpected capacity to simultaneously bind four copies of DHEA-S. Two DHEA-S molecules are located in the active site proper, one in a ligand access channel, and one on the hydrophobic F'-G' surface normally embedded in the membrane. While neither DHEA-S binding nor metabolism exhibit cooperative kinetics, the current structure is consistent with cooperativity common to CYP3A enzymes. Overall, this information suggests that mechanism(s) of CYP3A7 interactions with steroidal substrates are complex.
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Affiliation(s)
- Jinghan Liu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Sylvie E Kandel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Jed N Lampe
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Emily E Scott
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Departments of Pharmacology, Biological Chemistry and Programs in Chemical Biology and Biophysics, University of Michigan, Ann Arbor, Michigan, USA.
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2
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Guengerich FP, McCarty KD, Tateishi Y, Liu L. Steroid 17α-hydroxylase/17, 20-lyase (cytochrome P450 17A1). Methods Enzymol 2023; 689:39-63. [PMID: 37802581 DOI: 10.1016/bs.mie.2023.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Cytochrome P450 (P450) 17A1 plays a key role in steroidogenesis, in that this enzyme catalyzes the 17α-hydroxylation of both pregnenolone and progesterone, followed by a lyase reaction to cleave the C-20 land C-21 carbons from each steroid. The reactions are important in the production of both glucocorticoids and androgens. The enzyme is critical in humans but is also a drug target in treatment of prostate cancer. Detailed methods are described for the heterologous expression of human P450 17A1 in bacteria, purification of the recombinant enzyme, reconstitution of the enzyme system in the presence of cytochrome b5, and chromatographic procedures for sensitive analyses of reaction products. Historic assay approaches are reviewed. Some information is also provided about outstanding questions in the research field, including catalytic mechanisms and searches for selective inhibitors.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States.
| | - Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Yasuhiro Tateishi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Lu Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
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3
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Denisov IG, Grinkova YV, Camp T, McLean MA, Sligar SG. Midazolam as a Probe for Drug-Drug Interactions Mediated by CYP3A4: Homotropic Allosteric Mechanism of Site-Specific Hydroxylation. Biochemistry 2021; 60:1670-1681. [PMID: 34015213 DOI: 10.1021/acs.biochem.1c00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We developed an efficient and sensitive probe for drug-drug interactions mediated by human CYP3A4 by using midazolam (MDZ) as a probe substrate. Using global analysis of four parameters over several experimental data sets, we demonstrate that the first MDZ molecule (MDZ1) binds with high affinity at the productive site near the heme iron and gives only hydroxylation at the 1 position (1OH). The second midazolam molecule (MDZ2) binds at an allosteric site at the membrane surface and perturbs the position and mobility of MDZ1 such that the minor hydroxylation product at the 4 position (4OH) is formed in a 1:2 ratio (35%). No increase in catalytic rate is observed after the second MDZ binding. Hence, the site of the 1OH:4OH metabolism ratio is a sensitive probe for drugs, such as progesterone, that bind with high affinity to the allosteric site and serve as effectors. We observe similar changes in the MDZ 1OH:4OH ratio in the presence of progesterone (PGS), suggesting a direct communication between the active and allosteric sites. Mutations introduced into the F-F' loop indicate that residues F213 and D214 are directly involved in allosteric interactions leading to MDZ homotropic cooperativity, and these same residues, together with L211, are involved in heterotropic allosteric interactions in which PGS is the effector and MDZ the substrate. Molecular dynamics simulations provide a mechanistic picture of the origin of this cooperativity. These results show that the midazolam can be used as a sensitive probe for drug-drug interactions in human P450 CYP3A4.
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4
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Guengerich FP, McCarty KD, Chapman JG. Kinetics of cytochrome P450 3A4 inhibition by heterocyclic drugs defines a general sequential multistep binding process. J Biol Chem 2021; 296:100223. [PMID: 33449875 PMCID: PMC7948456 DOI: 10.1074/jbc.ra120.016855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/21/2022] Open
Abstract
Cytochrome P450 (P450) 3A4 is the enzyme most involved in the metabolism of drugs and can also oxidize numerous steroids. This enzyme is also involved in one-half of pharmacokinetic drug-drug interactions, but details of the exact mechanisms of P450 3A4 inhibition are still unclear in many cases. Ketoconazole, clotrimazole, ritonavir, indinavir, and itraconazole are strong inhibitors; analysis of the kinetics of reversal of inhibition with the model substrate 7-benzoyl quinoline showed lag phases in several cases, consistent with multiple structures of P450 3A4 inhibitor complexes. Lags in the onset of inhibition were observed when inhibitors were added to P450 3A4 in 7-benzoyl quinoline O-debenzylation reactions, and similar patterns were observed for inhibition of testosterone 6β-hydroxylation by ritonavir and indinavir. Upon mixing with inhibitors, P450 3A4 showed rapid binding as judged by a spectral shift with at least partial high-spin iron character, followed by a slower conversion to a low-spin iron-nitrogen complex. The changes were best described by two intermediate complexes, one being a partial high-spin form and the second another intermediate, with half-lives of seconds. The kinetics could be modeled in a system involving initial loose binding of inhibitor, followed by a slow step leading to a tighter complex on a multisecond time scale. Although some more complex possibilities cannot be dismissed, these results describe a system in which conformationally distinct forms of P450 3A4 bind inhibitors rapidly and two distinct P450-inhibitor complexes exist en route to the final enzyme-inhibitor complex with full inhibitory activity.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| | - Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jesse G Chapman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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5
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Redhair M, Hackett JC, Pelletier RD, Atkins WM. Dynamics and Location of the Allosteric Midazolam Site in Cytochrome P4503A4 in Lipid Nanodiscs. Biochemistry 2020; 59:766-779. [PMID: 31961139 DOI: 10.1021/acs.biochem.9b01001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Promiscuous and allosteric drug interactions with cytochrome P450 3A4 (CYP3A4) are ubiquitous but incompletely understood at the molecular level. A classic allosteric CYP3A4 drug interaction includes the benzodiazepine midazolam (MDZ). MDZ exhibits homotropic and heterotropic allostery when metabolized to 1'-hydroxy and 4-hydroxy metabolites in varying ratios. The combination of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and Gaussian accelerated molecular dynamics (GaMD) simulations of CYP3A4 in lipid nanodiscs and in a lipid bilayer, respectively, reveals MDZ-dependent changes in dynamics in a membrane environment. The F-, G-, and intervening helices, as well as the loop preceding the β1-sheets, display the largest observed changes in HDX. The GaMD suggests a potential allosteric binding site for MDZ in the F'- and G'-regions, which undergo significant increases in HDX at near-saturating MDZ concentrations. The HDX-MS and GaMD results confirm that changes in dynamics are most significant near the developing consensus allosteric site, and these changes are distinct from those observed previously with the nonallosteric inhibitor ketoconazole. The results suggest that the allosteric MDZ remains mobile in its binding site at the Phe-cluster. The results further suggest that this binding site remains dynamic or changes the depth of insertion in the membrane.
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Affiliation(s)
- Michelle Redhair
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195-7610 , United States
| | - John C Hackett
- Department of Physiology and Biophysics and the Massey Cancer Center, School of Medicine , Virginia Commonwealth University , Richmond , Virginia 23298-0035 , United States
| | - Robert D Pelletier
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195-7610 , United States
| | - William M Atkins
- Department of Medicinal Chemistry , University of Washington , Seattle , Washington 98195-7610 , United States
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6
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Mahajan M, Ravula T, Prade E, Anantharamaiah GM, Ramamoorthy A. Probing membrane enhanced protein-protein interactions in a minimal redox complex of cytochrome-P450 and P450-reductase. Chem Commun (Camb) 2019; 55:5777-5780. [PMID: 31041432 PMCID: PMC7467500 DOI: 10.1039/c9cc01630a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Investigating the interplay in a minimal redox complex of cytochrome-P450 and its reductase is crucial for understanding cytochrome-P450's enzymatic activity. Probing the hotspots of dynamic structural interactions using NMR revealed the engagement of loop residues from P450-reductase to be responsible for the enhanced affinity of CYP450 towards its obligate redox partner.
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Affiliation(s)
- Mukesh Mahajan
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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7
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Barnaba C, Ramamoorthy A. Picturing the Membrane-assisted Choreography of Cytochrome P450 with Lipid Nanodiscs. Chemphyschem 2018; 19:2603-2613. [DOI: 10.1002/cphc.201800444] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Carlo Barnaba
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor, MI 48109-1055 USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor, MI 48109-1055 USA
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8
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Ravula T, Barnaba C, Mahajan M, Anantharamaiah GM, Im SC, Waskell L, Ramamoorthy A. Membrane environment drives cytochrome P450's spin transition and its interaction with cytochrome b 5. Chem Commun (Camb) 2018; 53:12798-12801. [PMID: 29143058 DOI: 10.1039/c7cc07520k] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heme's spin-multiplicity is key in determining the enzymatic function of cytochrome P450 (cytP450). The origin of the low-spin state in ferric P450 is still under debate. Here, we report the first experimental demonstration of P450's membrane interaction altering its spin equilibrium which is accompanied by a stronger affinity for cytochrome b5. These results highlight the importance of lipid membrane for the function of P450.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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9
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Barnaba C, Gentry K, Sumangala N, Ramamoorthy A. The catalytic function of cytochrome P450 is entwined with its membrane-bound nature. F1000Res 2017; 6:662. [PMID: 28529725 PMCID: PMC5428493 DOI: 10.12688/f1000research.11015.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2017] [Indexed: 12/21/2022] Open
Abstract
Cytochrome P450, a family of monooxygenase enzymes, is organized as a catalytic metabolon, which requires enzymatic partners as well as environmental factors that tune its complex dynamic. P450 and its reducing counterparts—cytochrome P450-reductase and cytochrome
b
5—are membrane-bound proteins located in the cytosolic side of the endoplasmic reticulum. They are believed to dynamically associate to form functional complexes. Increasing experimental evidence signifies the role(s) played by both protein-protein and protein-lipid interactions in P450 catalytic function and efficiency. However, the biophysical challenges posed by their membrane-bound nature have severely limited high-resolution understanding of the molecular interfaces of these interactions. In this article, we provide an overview of the current knowledge on cytochrome P450, highlighting the environmental factors that are entwined with its metabolic function. Recent advances in structural biophysics are also discussed, setting up the bases for a new paradigm in the study of this important class of membrane-bound enzymes.
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Affiliation(s)
- Carlo Barnaba
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Katherine Gentry
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Nirupama Sumangala
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, MI, USA
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10
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Barnaba C, Martinez MJ, Taylor E, Barden AO, Brozik JA. Single-Protein Tracking Reveals That NADPH Mediates the Insertion of Cytochrome P450 Reductase into a Biomimetic of the Endoplasmic Reticulum. J Am Chem Soc 2017; 139:5420-5430. [PMID: 28347139 DOI: 10.1021/jacs.7b00663] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cytochrome P450 reductase (CPR) is the redox partner for most human cytochrome P450 enzymes. It is also believed that CPR is an integral membrane protein exclusively. Herein, we report that, contrary to this belief, CPR can exist as a peripheral membrane protein in the absence of NADPH and will transition to an integral membrane protein in the presence of stoichiometric amounts of NADPH or greater. All experiments were performed in a solid-supported cushioned lipid bilayer that closely matched the chemical composition of the human endoplasmic reticulum and served as an ER biomimetic. The phase characteristics and fluidity of the ER biomimetic was characterized with fluorescence micrographs and temperature-dependent fluorescence recovery after photobleaching. The interactions of CPR with the ER biomimetic were directly observed by tracking single CPR molecules using time-lapse single-molecule fluorescence imaging and subsequent analysis of tracks. These studies revealed dramatic changes in diffusion coefficient and the degree of partitioning of CPR as a function of NADPH concentration.
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Affiliation(s)
- Carlo Barnaba
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
| | - Michael J Martinez
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
| | - Evan Taylor
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
| | - Adam O Barden
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
| | - James A Brozik
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164-4630, United States
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11
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Bioactivation and Regioselectivity of Pig Cytochrome P450 3A29 towards Aflatoxin B₁. Toxins (Basel) 2016; 8:toxins8090267. [PMID: 27626447 PMCID: PMC5037493 DOI: 10.3390/toxins8090267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/05/2016] [Indexed: 01/10/2023] Open
Abstract
Due to unavoidable contaminations in feedstuff, pigs are easily exposed to aflatoxin B1 (AFB1) and suffer from poisoning, thus the poisoned products potentially affect human health. Heretofore, the metabolic process of AFB1 in pigs remains to be clarified, especially the principal cytochrome P450 oxidases responsible for its activation. In this study, we cloned CYP3A29 from pig liver and expressed it in Escherichia coli, and its activity has been confirmed with the typical P450 CO-reduced spectral characteristic and nifedipine-oxidizing activity. The reconstituted membrane incubation proved that the recombinant CYP3A29 was able to oxidize AFB1 to form AFB1-exo-8,9-epoxide in vitro. The structural basis for the regioselective epoxidation of AFB1 by CYP3A29 was further addressed. The T309A mutation significantly decreased the production of AFBO, whereas F304A exhibited an enhanced activation towards AFB1. In agreement with the mutagenesis study, the molecular docking simulation suggested that Thr309 played a significant role in stabilization of AFB1 binding in the active center through a hydrogen bond. In addition, the bulk phenyl group of Phe304 potentially imposed steric hindrance on the binding of AFB1. Our study demonstrates the bioactivation of pig CYP3A29 towards AFB1 in vitro, and provides the insight for understanding regioselectivity of CYP3A29 to AFB1.
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Trubetskoy OV, Gibson JR, Marks BD. Highly Miniaturized Formats for In Vitro Drug Metabolism Assays Using Vivid® Fluorescent Substrates and Recombinant Human Cytochrome P450 Enzymes. ACTA ACUST UNITED AC 2016; 10:56-66. [PMID: 15695344 DOI: 10.1177/1087057104269731] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Highly miniaturized P450 screening assays designed to enable facile analysis of P450 drug interactions in a 1536-well plate format with the principal human cytochrome P450 enzymes (CYP3A4, 2D6, 2C9, 2C19, and 1A2) and Vivid® fluorogenic substrates were developed. The detailed characterization of the assays included stability, homogeneity, and reproducibility of the recombinant P450 enzymes and the kinetic parameters of their reactions with Vivid® fluorogenic substrates, with a focus on the specific characteristics of each component that enable screening in a low-volume 1536-well plate assay format. The screening assays were applied for the assessment of individual cytochrome P450 inhibition profiles with a panel of selected assay modifiers, including isozyme-specific substrates and inhibitors. IC50values obtained for the modifiers in 96- and 1536-well plate formats were similar and comparable with values obtained in assays with conventional substrates. An overall examination of the 1536-well assay statistics, such as signal-to-background ratio and Z′ factor, demonstrated that these assays are a robust, successful, and reliable tool to screen for cytochrome P450 metabolism and inhibition in an ultra-high-throughput screening format. ( Journal of Biomolecular Screening 2005:56-66)
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13
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Barnaba C, Humphreys SC, Barden AO, Jones JP, Brozik JA. Substrate Dependent Native Luminescence from Cytochromes P450 3A4, 2C9, and P450cam. J Phys Chem B 2016; 120:3038-3047. [PMID: 26939024 DOI: 10.1021/acs.jpcb.5b11804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metalloporphyrin containing proteins, such as cytochrome P450, play a key role in biological systems. The spectroscopic properties of metalloporphyrins have been a subject of intense interest and intense debate for over 50 years. Iron-porphyrins are usually believed to be nonfluorescent. Herein we report that, contrary to this belief, cytochrome P450 heme groups luminesce with enough intensity to be of use in the characterization of these enzymes. To confirm that the emission is from the heme, we destroyed the heme by titration with cumene hydroperoxide and measured the changes in emission upon titration with compounds known to bind to the distal face of the heme in two human cytochrome P450 enzymes, known as CYP3A4 and CYP2C9. The titration curves gave spectral dissociation constants that were not significantly different from those reported using the Soret UV/vis absorbance changes. We have tentatively assigned the broad luminescence at ∼500 nm to a (1)ππ* → gs fluorescence and the structured luminescence above 600 nm to a (3)ππ* → gs phosphorescence. These assignments are not associated with the Q-band, and are in violation of Kasha's rule. To illustrate the utility of the emission, we measured spectral dissociation constants for testosterone binding to P450 3A4 in bilayers formed on glass coverslips, a measurement that would be very difficult to make using absorption spectroscopy. Complementary experiments were carried out with water-soluble P450cam.
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Affiliation(s)
- Carlo Barnaba
- Washington State University, Department of Chemistry, PO Box 644630, Pullman, WA, USA, 99164-4630
| | - Sara C Humphreys
- Washington State University, Department of Chemistry, PO Box 644630, Pullman, WA, USA, 99164-4630
| | - Adam O Barden
- Washington State University, Department of Chemistry, PO Box 644630, Pullman, WA, USA, 99164-4630
| | - Jeffrey P Jones
- Washington State University, Department of Chemistry, PO Box 644630, Pullman, WA, USA, 99164-4630
| | - James A Brozik
- Washington State University, Department of Chemistry, PO Box 644630, Pullman, WA, USA, 99164-4630
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14
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Rock BM, Hengel SM, Rock DA, Wienkers LC, Kunze KL. Characterization of ritonavir-mediated inactivation of cytochrome P450 3A4. Mol Pharmacol 2014; 86:665-74. [PMID: 25274602 DOI: 10.1124/mol.114.094862] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Ritonavir is a human immunodeficiency virus (HIV) protease inhibitor and an inhibitor of cytochrome P450 3A4, the major human hepatic drug-metabolizing enzyme. Given the potent inhibition of CYP3A4 by ritonavir, subtherapeutic doses of ritonavir are used to increase plasma concentrations of other HIV drugs oxidized by CYP3A4, thereby extending their clinical efficacy. However, the mechanism of inhibition of CYP3A4 by ritonavir remains unclear. To date, data suggests multiple types of inhibition by ritonavir, including mechanism-based inactivation by metabolic-intermediate complex formation, competitive inhibition, irreversible type II coordination to the heme iron, and more recently heme destruction. The results presented here demonstrate that inhibition of CYP3A4 by ritonavir occurs by CYP3A4-mediated activation and subsequent formation of a covalent bond to the apoprotein. Incubations of [(3)H]ritonavir with reconstituted CYP3A4 and human liver microsomes resulted in a covalent binding stoichiometry equal to 0.93 ± 0.04 moles of ritonavir bound per mole of inactivated CYP3A4. The metabolism of [(3)H]ritonavir by CYP3A4 leads to the formation of a covalent adduct specifically to CYP3A4, confirmed by radiometric liquid chromatography-trace and whole-protein mass spectrometry. Tryptic digestion of the CYP3A4-[(3)H]ritonavir incubations exhibited an adducted peptide (255-RM K: ESRLEDTQKHR-268) associated with a radiochromatic peak and a mass consistent with ritonavir plus 16 Da, in agreement with the whole-protein mass spectrometry. Additionally, nucleophilic trapping agents and scavengers of free oxygen species did not prevent inactivation of CYP3A4 by ritonavir. In conclusion, ritonavir exhibited potent time-dependent inactivation of CYP3A, with the mechanism of inactivation occurring though a covalent bond to Lys257 of the CYP3A4 apoprotein.
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Affiliation(s)
- Brooke M Rock
- Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., Seattle, Washington (B.M.R., D.A.R., L.C.W.); and Department of Medicinal Chemistry, University of Washington, Seattle, Washington (S.M.H., K.L.K.)
| | - Shawna M Hengel
- Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., Seattle, Washington (B.M.R., D.A.R., L.C.W.); and Department of Medicinal Chemistry, University of Washington, Seattle, Washington (S.M.H., K.L.K.)
| | - Dan A Rock
- Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., Seattle, Washington (B.M.R., D.A.R., L.C.W.); and Department of Medicinal Chemistry, University of Washington, Seattle, Washington (S.M.H., K.L.K.)
| | - Larry C Wienkers
- Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., Seattle, Washington (B.M.R., D.A.R., L.C.W.); and Department of Medicinal Chemistry, University of Washington, Seattle, Washington (S.M.H., K.L.K.)
| | - Kent L Kunze
- Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., Seattle, Washington (B.M.R., D.A.R., L.C.W.); and Department of Medicinal Chemistry, University of Washington, Seattle, Washington (S.M.H., K.L.K.)
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15
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Zhao C, Gao Q, Roberts AG, Shaffer SA, Doneanu CE, Xue S, Goodlett DR, Nelson SD, Atkins WM. Cross-linking mass spectrometry and mutagenesis confirm the functional importance of surface interactions between CYP3A4 and holo/apo cytochrome b(5). Biochemistry 2012; 51:9488-500. [PMID: 23150942 DOI: 10.1021/bi301069r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome b(5) (cyt b(5)) is one of the key components in the microsomal cytochrome P450 monooxygenase system. Consensus has not been reached about the underlying mechanism of cyt b(5) modulation of CYP catalysis. Both cyt b(5) and apo b(5) are reported to stimulate the activity of several P450 isoforms. In this study, the surface interactions of both holo and apo b(5) with CYP3A4 were investigated and compared for the first time. Chemical cross-linking coupled with mass spectrometric analysis was used to identify the potential electrostatic interactions between the protein surfaces. Subsequently, the models of interaction of holo/apo b(5) with CYP3A4 were built using the identified interacting sites as constraints. Both cyt b(5) and apo b(5) were predicted to bind to the same groove on CYP3A4 with close contacts to the B-B' loop of CYP3A4, a substrate recognition site. Mutagenesis studies further confirmed that the interacting sites on CYP3A4 (Lys96, Lys127, and Lys421) are functionally important. Mutation of these residues reduced or abolished cyt b(5) binding affinity. The critical role of Arg446 on CYP3A4 in binding to cyt b(5) and/or cytochrome P450 reductase was also discovered. The results indicated that electrostatic interactions on the interface of the two proteins are functionally important. The results indicate that apo b(5) can dock with CYP3A4 in a manner analogous to that of holo b(5), so electron transfer from cyt b(5) is not required for its effects.
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Affiliation(s)
- Chunsheng Zhao
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, USA
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16
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Schumacher SD, Jose J. Expression of active human P450 3A4 on the cell surface of Escherichia coli by Autodisplay. J Biotechnol 2012; 161:113-20. [DOI: 10.1016/j.jbiotec.2012.01.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 01/17/2012] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
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17
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Peng CC, Shi W, Lutz JD, Kunze KL, Liu JO, Nelson WL, Isoherranen N. Stereospecific metabolism of itraconazole by CYP3A4: dioxolane ring scission of azole antifungals. Drug Metab Dispos 2011; 40:426-35. [PMID: 22106171 DOI: 10.1124/dmd.111.042739] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Itraconazole (ITZ) is a mixture of four cis-stereoisomers that inhibit CYP3A4 potently and coordinate CYP3A4 heme via the triazole nitrogen. However, (2R,4S,2'R)-ITZ and (2R,4S,2'S)-ITZ also undergo stereoselective sequential metabolism by CYP3A4 at a site distant from the triazole ring to 3'-OH-ITZ, keto-ITZ, and N-desalkyl-ITZ. This stereoselective metabolism demonstrates specific interactions of ITZ within the CYP3A4 active site. To further investigate this process, the binding and metabolism of the four trans-ITZ stereoisomers by CYP3A4 were characterized. All four trans-ITZ stereoisomers were tight binding inhibitors of CYP3A4-mediated midazolam hydroxylation (IC(50) 16-26 nM), and each gave a type II spectrum upon binding to CYP3A4. However, instead of formation of 3'-OH-ITZ, they were oxidized at the dioxolane ring, leading to ring scission and formation of two new metabolites of ITZ. These two metabolites were also formed from the four cis-ITZ stereoisomers, although not as efficiently. The catalytic rates of dioxolane ring scission were similar to the dissociation rates of ITZ stereoisomers from CYP3A4, suggesting that the heme iron is reduced while the triazole moiety coordinates to it and no dissociation of ITZ is necessary before catalysis. The triazole containing metabolite [1-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-yl)ethanone] also inhibited CYP3A4 (IC(50) >15 μM) and showed type II binding with CYP3A4. The dioxolane ring scission appears to be clinically relevant because this metabolite was detected in urine samples from subjects that had been administered the mixture of cis-ITZ isomers. These data suggest that the dioxolane ring scission is a metabolic pathway for drugs that contain this moiety.
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Affiliation(s)
- Chi-Chi Peng
- Department of Pharmaceutics, University of Washington, P.O. Box 357610, Seattle, Washington 98103, USA
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18
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Cooperativity in monomeric enzymes with single ligand-binding sites. Bioorg Chem 2011; 43:44-50. [PMID: 22137502 DOI: 10.1016/j.bioorg.2011.11.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/04/2011] [Accepted: 11/05/2011] [Indexed: 11/21/2022]
Abstract
Cooperativity is widespread in biology. It empowers a variety of regulatory mechanisms and impacts both the kinetic and thermodynamic properties of macromolecular systems. Traditionally, cooperativity is viewed as requiring the participation of multiple, spatially distinct binding sites that communicate via ligand-induced structural rearrangements; however, cooperativity requires neither multiple ligand binding events nor multimeric assemblies. An underappreciated manifestation of cooperativity has been observed in the non-Michaelis-Menten kinetic response of certain monomeric enzymes that possess only a single ligand-binding site. In this review, we present an overview of kinetic cooperativity in monomeric enzymes. We discuss the primary mechanisms postulated to give rise to monomeric cooperativity and highlight modern experimental methods that could offer new insights into the nature of this phenomenon. We conclude with an updated list of single subunit enzymes that are suspected of displaying cooperativity, and a discussion of the biological significance of this unique kinetic response.
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19
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Woods CM, Fernandez C, Kunze KL, Atkins WM. Allosteric activation of cytochrome P450 3A4 by α-naphthoflavone: branch point regulation revealed by isotope dilution analysis. Biochemistry 2011; 50:10041-51. [PMID: 22004098 DOI: 10.1021/bi2013454] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the dominant xenobiotic metabolizing CYP. Despite great interest in CYP enzymology, two in vitro aspects of CYP3A4 catalysis are still not well understood, namely, sequential metabolism and allosteric activation. We have therefore investigated such a system in which both phenomena are present. Here we report that the sequential metabolism of Nile Red (NR) is accelerated by the heterotropic allosteric effector α-naphthoflavone (ANF). ANF increases the rates of formation for NR metabolites M1 and M2 and also perturbs the metabolite ratio in favor of M2. Thus, ANF has as an allosteric effect on a kinetic branch point. Co-incubating deuterium-labeled NR and unlabeled M1, we show that ANF increases k(cat)/k(off) ~1.8-fold in favor of the k(cat) of M2 production. Steady-state metabolic experiments are analyzed using a kinetic model in which the enzyme and substrates are not in rapid equilibrium, and this distinction allows for the estimation of rates of catalysis for the formation of both the primary (M1) and secondary (M2) products, as well as the partitioning of enzyme between these states. These results are compared with those of earlier spectroscopic investigations of NR and ANF cooperativity, and a mechanism of ANF heteroactivation is presented that involves effects on substrate off rate and coupling efficiency.
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Affiliation(s)
- Caleb M Woods
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195-7610, USA
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20
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Shinkyo R, Xu L, Tallman KA, Cheng Q, Porter NA, Guengerich FP. Conversion of 7-dehydrocholesterol to 7-ketocholesterol is catalyzed by human cytochrome P450 7A1 and occurs by direct oxidation without an epoxide intermediate. J Biol Chem 2011; 286:33021-8. [PMID: 21813643 PMCID: PMC3190903 DOI: 10.1074/jbc.m111.282434] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/01/2011] [Indexed: 11/06/2022] Open
Abstract
7-Ketocholesterol is a bioactive sterol, a potent competitive inhibitor of cytochrome P450 7A1, and toxic in liver cells. Multiple origins of this compound have been identified, with cholesterol being the presumed precursor. Although routes for formation of the 7-keto compound from cholesterol have been established, we found that 7-dehydrocholesterol (the immediate precursor of cholesterol) is oxidized by P450 7A1 to 7-ketocholesterol (k(cat)/K(m) = 3 × 10(4) m(-1) s(-1)). P450 7A1 converted lathosterol (Δ(5)-dihydro-7-dehydrocholesterol) to a mixture of the 7-keto and 7α,8α-epoxide products (~1:2 ratio), with the epoxide not rearranging to the ketone. The oxidation of 7-dehydrocholesterol occured with predominant formation of 7-ketocholesterol and with the 7α,8α-epoxide as only a minor product; the synthesized epoxide was stable in the presence of P450 7A1. The mechanism of 7-dehydrocholesterol oxidation to 7-ketocholesterol is proposed to involve a Fe(III)-O-C-C(+) intermediate and a 7,8-hydride shift or an alternative closing to yield the epoxide (Liebler, D. C., and Guengerich, F. P. (1983) Biochemistry 22, 5482-5489). Accordingly, reaction of P450 7A1 with 7-[(2)H(1)]dehydrocholesterol yielded complete migration of deuterium in the product 7-ketocholesterol. The finding that 7-dehydrocholesterol is a precursor of 7-ketocholesterol has relevance to an inborn error of metabolism known as Smith-Lemli-Opitz syndrome (SLOS) caused by defective cholesterol biosynthesis. Mutations within the gene encoding 7-dehydrocholesterol reductase, the last enzyme in the pathway, lead to the accumulation of 7-dehydrocholesterol in tissues and fluids of SLOS patients. Our findings suggest that 7-ketocholesterol levels may also be elevated in SLOS tissue and fluids as a result of P450 7A1 oxidation of 7-dehydrocholesterol.
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Affiliation(s)
| | | | | | - Qian Cheng
- To whom correspondence should be addressed: Dept. of Biochemistry, Vanderbilt University School of Medicine, 638 Robinson Research Bldg., 2200 Pierce Ave., Nashville, TN 37232-0146. Tel.: 615-322-2261; Fax: 615-322-3141; E-mail:
| | - Ned A. Porter
- From the Departments of Biochemistry and
- Chemistry and
- Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - F. Peter Guengerich
- From the Departments of Biochemistry and
- Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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21
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Rowland Yeo K, Walsky R, Jamei M, Rostami-Hodjegan A, Tucker G. Prediction of time-dependent CYP3A4 drug–drug interactions by physiologically based pharmacokinetic modelling: Impact of inactivation parameters and enzyme turnover. Eur J Pharm Sci 2011; 43:160-73. [DOI: 10.1016/j.ejps.2011.04.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 04/05/2011] [Accepted: 04/14/2011] [Indexed: 11/25/2022]
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22
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Pearson J, Dahal UP, Rock D, Peng CC, Schenk JO, Joswig-Jones C, Jones JP. The kinetic mechanism for cytochrome P450 metabolism of type II binding compounds: evidence supporting direct reduction. Arch Biochem Biophys 2011; 511:69-79. [PMID: 21530484 DOI: 10.1016/j.abb.2011.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 04/13/2011] [Accepted: 04/14/2011] [Indexed: 11/17/2022]
Abstract
The metabolic stability of a drug is an important property that should be optimized during drug design and development. Nitrogen incorporation is hypothesized to increase the stability by coordination of nitrogen to the heme iron of cytochrome P450, a binding mode that is referred to as type II binding. However, we noticed that the type II binding compound 1 has less metabolic stability at sub-saturating conditions than a closely related type I binding compound 3. Three kinetic models will be presented for type II binder metabolism; (1) Dead-end type II binding, (2) a rapid equilibrium between type I and II binding modes before reduction, and (3) a direct reduction of the type II coordinated heme. Data will be presented on reduction rates of iron, the off rates of substrate (using surface plasmon resonance) and the catalytic rate constants. These data argue against the dead-end, and rapid equilibrium models, leaving the direct reduction kinetic mechanism for metabolism of the type II binding compound 1.
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Affiliation(s)
- Joshua Pearson
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., Seattle, WA 98119, United States
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23
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Shinkyo R, Guengerich FP. Inhibition of human cytochrome P450 3A4 by cholesterol. J Biol Chem 2011; 286:18426-33. [PMID: 21471209 DOI: 10.1074/jbc.m111.240457] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
If cholesterol is a substrate of P450 3A4, then it follows that it should also be an inhibitor, particularly in light of the high concentrations found in liver. Heme perturbation spectra indicated a K(d) value of 8 μM for the P450 3A4-cholesterol complex. Cholesterol inhibited the P450 3A4-catalyzed oxidations of nifedipine and quinidine, two prototypic substrates, in liver microsomes and a reconstituted enzyme system with K(i) ∼ 10 μM in an apparently non-competitive manner. The concentration of cholesterol could be elevated 4-6-fold in cultured human hepatocytes by incubation with cholesterol; the level of P450 3A4 and cell viability were not altered under the conditions used. Nifedipine oxidation was inhibited when the cholesterol level was increased. We conclude that cholesterol is both a substrate and an inhibitor of P450 3A4, and a model is presented to explain the kinetic behavior. We propose that the endogenous cholesterol in hepatocytes should be considered in models of prediction of metabolism of drugs and steroids, even in the absence of changes in the concentrations of free cholesterol.
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Affiliation(s)
- Raku Shinkyo
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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24
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Production of human phase 1 and 2 metabolites by whole-cell biotransformation with recombinant microbes. Bioanalysis 2011; 2:1277-90. [PMID: 21083240 DOI: 10.4155/bio.10.80] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cytochrome P450 enzymes (CYPs or P450s) are the most important enzymes involved in the phase I metabolism of drugs and poisons in humans, while UDP glycosyltransferases catalyze the majority of phase II reactions. In addition, a number of other enzymes or enzyme families contribute to the metabolism of xenobiotica, including alcohol dehydrogenase, aldehyde dehydrogenase, ester and amide hydrolases, epoxide hydrolase and flavine monooxygenases, as well as sulfotransferases, catechol-O-methyltransferase and N-acetyltransferase. A thorough understanding of their activity and of the properties of the metabolites they form is an essential prerequisite for the assessment of drug-caused side effects or toxicity. In this context of MIST, efficient production systems are needed to permit the large-scale production of human drug metabolites. As classical chemical synthesis cannot always provide these metabolites, biotechnological approaches have been developed that typically employ the recombinant expression of human drug-metabolizing enzymes. This review summarizes the current knowledge regarding whole-cell biotransformation processes that make use of such an approach.
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25
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Shinkyo R, Guengerich FP. Cytochrome P450 7A1 cholesterol 7alpha-hydroxylation: individual reaction steps in the catalytic cycle and rate-limiting ferric iron reduction. J Biol Chem 2010; 286:4632-43. [PMID: 21147774 DOI: 10.1074/jbc.m110.193409] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) 7A1 is well known as the cholesterol 7α-hydroxylase, the first enzyme involved in bile acid synthesis from cholesterol. The human enzyme has been reported to have the highest catalytic activity of any mammalian P450. Analyses of individual steps of cholesterol 7α-hydroxylation reaction revealed several characteristics of this reaction: (i) two-step binding of cholesterol to ferric P450, with an apparent K(d) of 0.51 μM, (ii) a rapid reduction rate in the presence of cholesterol (∼10 s(-1) for the fast phase), (iii) rapid formation of a ferrous P450-cholesterol-O(2) complex (29 s(-1)), (iv) the lack of a non-competitive kinetic deuterium isotope effect, (v) the lack of a kinetic burst, and (vi) the lack of a deuterium isotope effect when the reaction was initiated with the ferrous P450-cholesterol complex. A minimum kinetic model was developed and is consistent with all of the observed phenomena and the rates of cholesterol 7α-hydroxylation and H(2)O and H(2)O(2) formation. The results indicate that the first electron transfer step, although rapid, becomes rate-limiting in the overall P450 7A1 reaction. This is a different phenomenon compared with other P450s that have much lower rates of catalysis, attributed to the much more efficient substrate oxidation steps in this reaction.
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Affiliation(s)
- Raku Shinkyo
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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26
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Nishida CR, Lee M, de Montellano PRO. Efficient hypoxic activation of the anticancer agent AQ4N by CYP2S1 and CYP2W1. Mol Pharmacol 2010; 78:497-502. [PMID: 20566689 DOI: 10.1124/mol.110.065045] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AQ4N [1,4-bis{[2-(dimethylamino-N-oxide)ethyl]amino}-5,8-dihydroxyanthracene-9,10-dione], a prodrug with two dimethylamino N-oxide groups, is converted to the topoisomerase II inhibitor AQ4 [1,4-bis{[2-(dimethylamino)ethyl]amino}-5,8-dihydroxy-anthracene-9,10-dione] by reduction of the N-oxides to dimethylamino substituents. Earlier studies showed that several drug-metabolizing cytochrome P450 (P450) enzymes can catalyze this reductive reaction under hypoxic conditions comparable with those in solid tumors. CYP2S1 and CYP2W1, two extrahepatic P450 enzymes identified from the human genome whose functions are unknown, are expressed in hypoxic tumor cells at much higher levels than in normal tissue. Here, we demonstrate that CYP2S1, contrary to a published report (Mol Pharmacol 76:1031-1043, 2009), is efficiently reduced by NADPH-P450 reductase. Most importantly, both CYP2S1 and CYP2W1 are better catalysts for the reductive activation of AQ4N to AQ4 than all previously examined P450 enzymes. The overexpression of CYP2S1 and CYP2W1 in tumor tissues, together with their high catalytic activities for AQ4N activation, suggests that they may be exploited for the localized activation of anticancer prodrugs.
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Affiliation(s)
- Clinton R Nishida
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
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27
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Grinkova YV, Denisov IG, Sligar SG. Functional reconstitution of monomeric CYP3A4 with multiple cytochrome P450 reductase molecules in Nanodiscs. Biochem Biophys Res Commun 2010; 398:194-8. [PMID: 20599740 DOI: 10.1016/j.bbrc.2010.06.058] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 06/11/2010] [Indexed: 11/26/2022]
Abstract
Traditional reconstitution of membrane cytochromes P450 monooxygenase system requires efficient solubilization of both P450 heme enzymes and redox partner NADPH dependent reductase, CPR, either in mixed micellar solution or by incorporation in liposomes. Here we describe a simple alternative approach to assembly of soluble complexes of monomeric human hepatic cytochrome P450 CYP3A4 with CPR by co-incorporation into nanoscale POPC bilayer Nanodiscs. Stable and fully functional complexes with different CPR:CYP3A4 stoichiometric ratios are formed within several minutes after addition of the full-length CPR to the solution of CYP3A4 preassembled into POPC Nanodiscs at 37 degrees C. We find that the steady state rates of NADPH oxidation and testosterone hydroxylation strongly depend on CPR:CYP3A4 ratio and reach maximum at tenfold molar access of CPR. The binding of CPR to CYP3A4 in Nanodiscs is tight, such that complexes with different stoichiometry can be separated by size-exclusion chromatography. Reconstitution systems based on the co-incorporation of CPR into preformed Nanodiscs with different human cytochromes P450 are suitable for high-throughput screening of substrates and inhibitors and for drug-drug interaction studies.
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Affiliation(s)
- Yelena V Grinkova
- Department of Biochemistry, School of Molecular and Cellular Biology, The University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801, USA
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28
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Pearson JT, Siu S, Meininger DP, Wienkers LC, Rock DA. In Vitro Modulation of Cytochrome P450 Reductase Supported Indoleamine 2,3-Dioxygenase Activity by Allosteric Effectors Cytochrome b5 and Methylene Blue. Biochemistry 2010; 49:2647-56. [DOI: 10.1021/bi100022c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Josh T. Pearson
- Biochemistry and Biophysics Group, Department of Pharmacokinetics and Drug Metabolism
| | | | | | - Larry C. Wienkers
- Biochemistry and Biophysics Group, Department of Pharmacokinetics and Drug Metabolism
| | - Dan A. Rock
- Biochemistry and Biophysics Group, Department of Pharmacokinetics and Drug Metabolism
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29
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Sohl CD, Cheng Q, Guengerich FP. Chromatographic assays of drug oxidation by human cytochrome P450 3A4. Nat Protoc 2009; 4:1252-7. [PMID: 19661995 PMCID: PMC3883453 DOI: 10.1038/nprot.2009.122] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cytochrome P450 enzymes (P450s) are heme-thiolate mono-oxygenases involved in the oxidation of many endogenous and exogenous substrates. Herein, we describe two protocols for measuring the activity of a key enzyme of drug metabolism, P450 3A4. In this protocol, the substrate is incubated with human liver microsomes, the reaction is quenched, and the substrates and products are extracted and subjected to liquid chromatography (LC) separation and detection. Oxidation of the calcium-channel blocker nifedipine is measured using UV-Vis spectroscopy in-line with high performance liquid chromatography (HPLC). 6beta-Hydroxytestosterone formation from testosterone is measured by HPLC coupled to mass spectrometry (MS). Both of these procedures are rapid, requiring 2 h or less, and can be used to confirm and measure P450 3A4 activity and can also be used as a guide for developing other assays for measuring P450 catalysis. The separation strategy described here is more rapid than many available methods, except when ultra-performance liquid chromatography (UPLC) is used.
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Affiliation(s)
- Christal D Sohl
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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30
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Jiang Y, Ortiz de Montellano PR. Cooperative effects on radical recombination in CYP3A4-catalyzed oxidation of the radical clock beta-thujone. Chembiochem 2009; 10:650-3. [PMID: 19189363 DOI: 10.1002/cbic.200800772] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The timing of the beta-thujone radical clock (see scheme) can be specifically altered by an allosteric effector. Progesterone, a well-documented CYP3A4 allosteric effector, was found to increase the yield of the unrearranged, C4-derived product of beta-thujone oxidation at the expense of the combined yields of all the rearranged C4-oxidized metabolites. The results demonstrate that the apparent radical recombination rate in the CYP3A4 hydroxylation of beta-thujone is accelerated by the progesterone heterotropic cooperativity.
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Affiliation(s)
- Yongying Jiang
- Department of Pharmaceutical Chemistry, University of California-San Francisco, 600 16th Street, San Francisco, CA 94158-2517, USA
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31
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DiMaio Knych H, DeStefano Shields C, Buckpitt A, Stanley S. Equine cytochrome P450 2C92: cDNA cloning, expression and initial characterization. Arch Biochem Biophys 2009; 485:49-55. [DOI: 10.1016/j.abb.2009.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 02/11/2009] [Accepted: 02/12/2009] [Indexed: 12/12/2022]
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32
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Peng CC, Cape JL, Rushmore T, Crouch GJ, Jones JP. Cytochrome P450 2C9 type II binding studies on quinoline-4-carboxamide analogues. J Med Chem 2009; 51:8000-11. [PMID: 19053752 DOI: 10.1021/jm8011257] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CYP2C9 is a significant P450 protein responsible for drug metabolism. With the increased use of heterocyclic compounds in drug design, a rapid and efficient predrug screening of these potential type II binding compounds is essential to avoid adverse drug reactions. To understand binding modes, we use quinoline-4-carboxamide analogues to study the factors that determine the structure-activity relationships. The results of this study suggest that the more accessible pyridine with the nitrogen para to the linkage can coordinate directly with the ferric heme iron, but this is not seen for the meta or ortho isomers. The pi-cation interaction of the naphthalene moiety and Arg 108 residue may also assist in stabilizing substrate binding within the active-site cavity. The type II substrate binding affinity is determined by the combination of steric, electrostatic, and hydrophobicity factors; meanwhile, it is enhanced by the strength of lone pair electrons coordination with the heme iron.
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Affiliation(s)
- Chi-Chi Peng
- Department of Chemistry, Washington State University, P.O. Box 644630, Pullman, Washington 99164-4630, USA
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33
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Development of immobilized enzyme reactors based on human recombinant cytochrome P450 enzymes for phase I drug metabolism studies. J Chromatogr A 2008; 1206:2-10. [DOI: 10.1016/j.chroma.2008.05.080] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 05/26/2008] [Accepted: 05/27/2008] [Indexed: 11/21/2022]
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34
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Rabe KS, Gandubert VJ, Spengler M, Erkelenz M, Niemeyer CM. Engineering and assaying of cytochrome P450 biocatalysts. Anal Bioanal Chem 2008; 392:1059-73. [PMID: 18622752 DOI: 10.1007/s00216-008-2248-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 06/11/2008] [Accepted: 06/12/2008] [Indexed: 11/29/2022]
Abstract
Cytochrome P450s constitute a highly fascinating superfamily of enzymes which catalyze a broad range of reactions. They are essential for drug metabolism and promise industrial applications in biotechnology and biosensing. The constant search for cytochrome P450 enzymes with enhanced catalytic performances has generated a large body of research. This review will concentrate on two key aspects related to the identification and improvement of cytochrome P450 biocatalysts, namely the engineering and assaying of these enzymes. To this end, recent advances in cytochrome P450 development are reported and commonly used screening methods are surveyed.
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Affiliation(s)
- Kersten S Rabe
- Fakultät für Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Otto-Hahn-Strabetae 6, 44227, Dortmund, Germany
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35
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Fernando H, Halpert JR, Davydov DR. Kinetics of electron transfer in the complex of cytochrome P450 3A4 with the flavin domain of cytochrome P450BM-3 as evidence of functional heterogeneity of the heme protein. Arch Biochem Biophys 2008; 471:20-31. [PMID: 18086551 PMCID: PMC2346489 DOI: 10.1016/j.abb.2007.11.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 11/10/2007] [Accepted: 11/30/2007] [Indexed: 11/18/2022]
Abstract
We used a rapid scanning stop-flow technique to study the kinetics of reduction of cytochrome P450 3A4 (CYP3A4) by the flavin domain of cytochrome P450-BM3 (BMR), which was shown to form a stoichiometric complex (K(D)=0.48 microM) with CYP3A4. In the absence of substrates only about 50% of CYP3A4 was able to accept electrons from BMR. Whereas the high-spin fraction was completely reducible, the reducibility of the low-spin fraction did not exceed 42%. Among four substrates tested (testosterone, 1-pyrenebutanol, bromocriptine, or alpha-naphthoflavone (ANF)) only ANF is capable of increasing the reducibility of the low-spin fraction to 75%. Our results demonstrate that the pool of CYP3A4 is heterogeneous, and not all P450 is competent for electron transfer in the complex with reductase. The increase in the reducibility of the enzyme in the presence of ANF may represent an important element of the mechanism of action of this activator.
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Affiliation(s)
- Harshica Fernando
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-1031
| | - James R. Halpert
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-1031
| | - Dmitri R. Davydov
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-1031
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Davydov DR, Davydova NY, Tsalkova TN, Halpert JR. Effect of glutathione on homo- and heterotropic cooperativity in cytochrome P450 3A4. Arch Biochem Biophys 2008; 471:134-45. [PMID: 18206979 DOI: 10.1016/j.abb.2008.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/31/2007] [Accepted: 01/06/2008] [Indexed: 11/27/2022]
Abstract
Glutathione (GSH) exerted a profound effect on the oxidation of 7-benzyloxy-4-(trifluoromethyl)coumarin (BFC) and 7-benzyloxyquinoline (BQ) by human liver microsomes as well as by CYP3A4-containing insect cell microsomes (Baculosomes). The cooperativity in O-debenzylation of both substrates is eliminated in the presence of 1-4mM GSH. Addition of GSH also increased the amplitude of the 1-PB induced spin shift with purified CYP3A4 and abolished the cooperativity of 1-PB or BFC binding. Changes in fluorescence of 6-bromoacetyl-2-dimethylaminonaphthalene attached to the cysteine-depleted mutant CYP3A4(C58,C64) suggest a GSH-induced conformational changes in proximity of alpha-helix A. Importantly, the K(S) value for formation of the GSH complex and the concentrations in which GSH decreases CYP3A4 cooperativity are consistent with the physiological concentrations of GSH in hepatocytes. Therefore, the allosteric effect of GSH on CYP3A4 may play an important role in regulation of microsomal monooxygenase activity in vivo.
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Affiliation(s)
- Dmitri R Davydov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-1031, USA.
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Purnapatre K, Khattar SK, Saini KS. Cytochrome P450s in the development of target-based anticancer drugs. Cancer Lett 2008; 259:1-15. [DOI: 10.1016/j.canlet.2007.10.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 10/16/2007] [Accepted: 10/17/2007] [Indexed: 11/16/2022]
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38
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Pearson JT, Wahlstrom JL, Dickmann LJ, Kumar S, Halpert JR, Wienkers LC, Foti RS, Rock DA. Differential Time-Dependent Inactivation of P450 3A4 and P450 3A5 by Raloxifene: A Key Role for C239 in Quenching Reactive Intermediates. Chem Res Toxicol 2007; 20:1778-86. [DOI: 10.1021/tx700207u] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Josh T. Pearson
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
| | - Jan L. Wahlstrom
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
| | - Leslie J. Dickmann
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
| | - Santosh Kumar
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
| | - James R. Halpert
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
| | - Larry C. Wienkers
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
| | - Robert S. Foti
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
| | - Dan A. Rock
- Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, and Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1031
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Cameron MD, Wen B, Roberts AG, Atkins WM, Campbell AP, Nelson SD. Cooperative binding of acetaminophen and caffeine within the P450 3A4 active site. Chem Res Toxicol 2007; 20:1434-41. [PMID: 17894464 DOI: 10.1021/tx7000702] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetaminophen (N-acetyl-p-aminophenol, APAP) is a commonly used analgesic/antipyretic. When oxidized by P450, a toxic APAP metabolite is generated. Human P450 3A4 was expressed in Escherichia coli , purified, and reconstituted using artificial liposomes. Oxidation of APAP by P450 3A4, as detected by the formation of its glutathione adduct, was found to exhibit negative homotropic cooperativity with a Hill coefficient of 0.7. In the presence of caffeine, the observed kinetics were close to classical Michaelis-Menten kinetics with a Hill coefficient approaching 1. In order to probe for a potential repositioning of APAP within the P450 3A4 pocket in the presence of caffeine, NMR T1 paramagnetic relaxation techniques were used to calculate distances from the P450 3A4 heme iron to protons of APAP alone and in the presence of caffeine. Both APAP and caffeine were found to bind at the active site in proximity to the heme iron. When APAP was incubated with P450 3A4, the acetamido group of APAP was found to be closest to the heme iron consistent with the amide group of APAP weakly associating with the heme iron. The addition of caffeine disrupted the ability of APAP to coordinate with the heme iron of P450 3A4 and enhanced the rate of oxidation to its toxic metabolite.
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Affiliation(s)
- Michael D Cameron
- Department of Medicinal Chemistry, University of Washington, Seattle 98195, USA
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40
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Nath A, Grinkova YV, Sligar SG, Atkins WM. Ligand binding to cytochrome P450 3A4 in phospholipid bilayer nanodiscs: the effect of model membranes. J Biol Chem 2007; 282:28309-28320. [PMID: 17573349 DOI: 10.1074/jbc.m703568200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound protein cytochrome P450 3A4 (CYP3A4) is a major drug-metabolizing enzyme. Most studies of ligand binding by CYP3A4 are currently carried out in solution, in the absence of a model membrane. Therefore, there is little information concerning the membrane effects on CYP3A4 ligand binding behavior. Phospholipid bilayer Nanodiscs are a novel model membrane system derived from high density lipoprotein particles, whose stability, monodispersity, and consistency are ensured by their self-assembly. We explore the energetics of four ligands (6-(p-toluidino)-2-naphthalenesulfonic acid (TNS), alpha-naphthoflavone (ANF), miconazole, and bromocriptine) binding to CYP3A4 incorporated into Nanodiscs. Ligand binding to Nanodiscs was monitored by a combination of environment-sensitive ligand fluorescence and ligand-induced shifts in the fluorescence of tryptophan residues present in the scaffold proteins of Nanodiscs; binding to the CYP3A4 active site was monitored by ligand-induced shifts in the heme Soret band absorbance. The dissociation constants for binding to the active site in CYP3A4-Nanodiscs were 4.0 microm for TNS, 5.8 microm for ANF, 0.45 microm for miconazole, and 0.45 microm for bromocriptine. These values are for CYP3A4 incorporated into a lipid bilayer and are therefore presumably more biologically relevant that those measured using CYP3A4 in solution. In some cases, affinity measurements using CYP3A4 in Nanodiscs differ significantly from solution values. We also studied the equilibrium between ligand binding to CYP3A4 and to the membrane. TNS showed no marked preference for either environment; ANF preferentially bound to the membrane, and miconazole and bromocriptine preferentially bound to the CYP3A4 active site.
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Affiliation(s)
- Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195
| | - Yelena V Grinkova
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195.
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41
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Kumar V, Rock DA, Warren CJ, Tracy TS, Wahlstrom JL. Enzyme source effects on CYP2C9 kinetics and inhibition. Drug Metab Dispos 2006; 34:1903-8. [PMID: 16928789 PMCID: PMC2377028 DOI: 10.1124/dmd.106.010249] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
When choosing a recombinant cytochrome P450 (P450) enzyme system for in vitro studies, it is critical to understand the strengths, limitations, and applicability of the enzyme system to the study design. Although literature kinetic data may be available to assist in enzyme system selection, comparison of data from separate laboratories is often confounded by differences in experimental conditions and bioanalytical techniques. We measured the Michaelis-Menten kinetic parameters for four CYP2C9 substrates (diclofenac, (S)-warfarin, tolbutamide, and (S)-flurbiprofen) using four recombinant CYP2C9 enzyme systems (Supersomes, Baculosomes, RECO system, and in-house purified, reconstituted enzyme) to determine whether the enzyme systems exhibited kinetic differences in metabolic product formation rates under uniform experimental conditions. The purified, reconstituted enzyme systems exhibited higher K(m) values, reduced substrate affinity, and lower calculated intrinsic clearance values compared with baculovirus microsomal preparations. Six- to 25-fold differences in predicted intrinsic clearance values were calculated for each substrate depending on the enzyme system-substrate combination. Results suggest that P450 reductase interactions with the CYP2C9 protein and varying ratios of CYP2C9/P450 reductase in the enzyme preparations may play a role in these observed differences. In addition, when (S)-flurbiprofen was used as a substrate probe to determine CYP2C9 inhibition with a set of 12 inhibitors, decreased inhibition potency was observed across 11 of those inhibitors in the RECO purified, reconstituted enzyme compared with the Supersomes baculovirus microsomal preparation and pooled human liver microsomes. Considering these differences, consistent use of an enzyme source is an important component in producing comparable and reproducible kinetics and inhibition data with CYP2C9.
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Affiliation(s)
- Vikas Kumar
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
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42
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Wen B, Lampe JN, Roberts AG, Atkins WM, David Rodrigues A, Nelson SD. Cysteine 98 in CYP3A4 contributes to conformational integrity required for P450 interaction with CYP reductase. Arch Biochem Biophys 2006; 454:42-54. [PMID: 16959210 PMCID: PMC2001172 DOI: 10.1016/j.abb.2006.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2006] [Revised: 07/31/2006] [Accepted: 08/01/2006] [Indexed: 10/24/2022]
Abstract
Previously human cytochrome P450 3A4 was efficiently and specifically photolabeled by the photoaffinity ligand lapachenole. One of the modification sites was identified as cysteine 98 in the B-C loop region of the protein [B. Wen, C.E. Doneanu, C.A. Gartner, A.G. Roberts, W.M. Atkins, S.D. Nelson, Biochemistry 44 (2005) 1833-1845]. Loss of CO binding capacity and subsequent decrease of catalytic activity were observed in the labeled CYP3A4, which suggested that aromatic substitution on residue 98 triggered a critical conformational change and subsequent loss of enzyme activity. To test this hypothesis, C98A, C98S, C98F, and C98W mutants were generated by site-directed mutagenesis and expressed functionally as oligohistidine-tagged proteins. Unlike the mono-adduction observed in the wild-type protein, simultaneous multiple adductions occurred when C98F and C98W were photolabeled under the same conditions as the wild-type enzyme, indicating a substantial conformational change in these two mutants compared with the wild-type protein. Kinetic analysis revealed that the C98W mutant had a drastic 16-fold decrease in catalytic efficiency (V(max)/K(m)) for 1'-OH midazolam formation, and about an 8-fold decrease in catalytic efficiency (V(max)/K(m)) for 4-OH midazolam formation, while the C98A and C98S mutants retained the same enzyme activity as the wild-type enzyme. Photolabeling of C98A and C98S with lapachenole resulted in monoadduction of only Cys-468, in contrast to the labeling of Cys-98 in wild-type CYP3A4, demonstrating the marked selectivity of this photoaffinity ligand for cysteine residues. The slight increases in the midazolam binding constants (K(s)) in these mutants suggested negligible perturbation of the heme environment. Further activity studies using different P450:reductase ratios suggested that the affinity of P450 to reductase was significantly decreased in the C98W mutant, but not in the C98A and C98S mutants. In addition, the C98W mutant exhibited a 41% decrease in the maximum electron flow rate between P450 and reductase as measured by reduced nicotinamide adenine dinucleotide phosphate consumption at a saturating reductase concentration. In conclusion, our data strongly suggest that cysteine 98 in the B-C loop region significantly contributes to conformational integrity and catalytic activity of CYP3A4, and that this residue or residues nearby might be involved in an interaction with P450 reductase.
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Affiliation(s)
- Bo Wen
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
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43
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Denisov IG, Grinkova YV, Baas BJ, Sligar SG. The ferrous-dioxygen intermediate in human cytochrome P450 3A4. Substrate dependence of formation and decay kinetics. J Biol Chem 2006; 281:23313-8. [PMID: 16762915 DOI: 10.1074/jbc.m605511200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The oxy-ferrous complex is the first of three branching intermediates in the catalytic cycle of cytochrome P450, in which the total efficiency of substrate turnover is curtailed by the side reaction of autoxidation. For human membrane-bound cytochromes P450, the oxy complex is believed to be the primary source of cytotoxic superoxide and peroxide, although information on the properties and stability of this intermediate is lacking. Here we document stopped-flow spectroscopic studies of the formation and decay of the oxy-ferrous complex in the most abundant human cytochrome P450 (CYP3A4) as a function of temperature in the substrate-free and substrate-bound form. CYP3A4 solubilized in purified monomeric form in nanoscale POPC bilayers is functionally and kinetically homogeneous. In substrate-free CYP3A4, the oxy complex is extremely unstable with a half-life of approximately 30 ms at 5 degrees C. Saturation with testosterone or bromocriptine stabilizes the oxy-ferrous intermediate. Comparison of the autoxidation rates with the available data on CYP3A4 turnover kinetics suggests that the oxy complex may be an important route for uncoupling.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana 61801, USA
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44
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Cheng J, Wan DF, Gu JR, Gong Y, Yang SL, Hao DC, Yang L. Establishment of a yeast system that stably expresses human cytochrome P450 reductase: Application for the study of drug metabolism of cytochrome P450s in vitro. Protein Expr Purif 2006; 47:467-76. [PMID: 16434211 DOI: 10.1016/j.pep.2005.11.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Revised: 11/20/2005] [Accepted: 11/25/2005] [Indexed: 11/30/2022]
Abstract
Cytochrome P450s (CYPs) hold a balance in studying pharmacokinetics, toxico-kinetics, drug metabolism, and drug-drug interactions, which require association with cytochrome P450 reductase (CPR) to achieve optimal activity. A novel system of Saccharomyces cerevisiae useful for expression studies of mammalian microsomal CYPs was established. Human CPR (hCPR) was co-expressed with human CYP3A4 (hCYP3A4) in this system, and two expression plasmids pTpLC and pYeplac195-3A4 containing the cDNA of hCPR and hCYP3A4 were constructed, respectively. The two plasmids were applied first and controlled by phosphoglycerate kinase (PGK) promoter. S. cerevisiae BWG1-7alpha transformed with the expression plasmids produced the respective proteins in the expected molecular sizes reactive with both anti-hCYP3A4 immunoglobulin (Ig) and anti-hCPR Ig. The activity of hCPR in yeast BWG-CPR was 443.2 nmol reduced cytochrome c/min/mg, which was about three times the CPR activity of the microsome prepared from the parental yeast. The protein amount of hCYP3A4 in BWG-CPR/3A4 was 35.53 pmol/mg, and the 6beta-hydroxylation testosterone formation activity of hCYP3A4 expressed was 7.5 nmol/min/nmol CYP, 30 times higher than the activity of hCYP3A4 expressed in the parental yeast, and almost two times the activity of hCYP3A4 from homologous human liver microsome. Meanwhile, BWG-CPR/3A4 retained 100 generations under nonselective culture conditions, indicating this yeast was a mitotically stable transformant. BWG-CPR was further tested daily by the PCR amplification of hCPR of yeast genome, Western blot analysis, and the activity assay of hCPR of yeast microsome. This special expression host for CYPs was validated to be stable and efficient for the expression of CYPs, applying as an effective selection model for the drug metabolism in vitro.
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Affiliation(s)
- Jie Cheng
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, No. 457, People's Republic of China
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45
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Wen B, Doneanu CE, Lampe JN, Roberts AG, Atkins WM, Nelson SD. Probing the CYP3A4 active site by cysteine scanning mutagenesis and photoaffinity labeling. Arch Biochem Biophys 2005; 444:100-11. [PMID: 16289363 DOI: 10.1016/j.abb.2005.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 09/21/2005] [Accepted: 09/22/2005] [Indexed: 11/18/2022]
Abstract
The mechanism of CYP3A4-substrate interactions has been investigated using a battery of techniques including cysteine scanning mutagenesis, photoaffinity labeling, and structural modeling. In this study, cysteine scanning mutagenesis was performed at seven sites within CYP3A4 proposed to be involved in substrate interaction and/or cooperativity. Photolabeled CYP3A4 peptide adducts were further characterized by mass spectrometric analysis for each mutant after proteolytic digestion and isolation of fluorescent photolabeled peptides. Among the tryptic peptides of seven tested mutants, three photolabeled peptides of the F108C mutant, ECYSVFTNR (positions 97-105), VLQNFSFKPCK (positions 459-469), and RPCGPVGFMK (positions 106-115) were identified by MALDI-TOF-MS and nano-LC/ESI QTOF MS. The site of modification was further localized to the substituted Cys-108 residue in the mutant peptide adduct RPCGPVGFMK (positions 106-115) by nano-LC/ESI QTOF MS/MS. In summary, we described a potentially useful method to study P450 active sites using a combination of cysteine scanning mutagenesis and photoaffinity labeling.
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Affiliation(s)
- Bo Wen
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA 98195, USA
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46
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Engtrakul JJ, Foti RS, Strelevitz TJ, Fisher MB. ALTERED AZT (3′-AZIDO-3′-DEOXYTHYMIDINE) GLUCURONIDATION KINETICS IN LIVER MICROSOMES AS AN EXPLANATION FOR UNDERPREDICTION OF IN VIVO CLEARANCE: COMPARISON TO HEPATOCYTES AND EFFECT OF INCUBATION ENVIRONMENT. Drug Metab Dispos 2005; 33:1621-7. [PMID: 16049128 DOI: 10.1124/dmd.105.005058] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human liver microsomes are a reagent commonly used to predict human hepatic clearance of new chemical entities via phase 1 metabolism. Another common metabolic pathway, glucuronidation, can also be observed in human liver microsomes, although the scalability of this process has not been validated. In fact, several groups have demonstrated that clearance estimated from liver microsomes with UDP-glucuronic acid typically underpredicts the actual in vivo clearance more than 10-fold for compounds that are predominantly glucuronidated. In contrast, clearance predicted using human hepatocytes, for these same compounds, provides a more accurate assessment of in vivo clearance. We sought to characterize the kinetics of glucuronidation of the selective UGT2B7 substrate AZT (3'-azido-3'-deoxythymidine), a selective UGT2B7 substrate, in human liver microsomes (HLMs), recombinant UGT2B7, and human hepatocytes. Apparent Km values in these three preparations were 760, 490, and 87 microM with apparent Vmax values highest in hepatocytes. The IC50 for ibuprofen against AZT glucuronidation, when run at its Km concentration in HLMs and hepatocytes, was 975 and 170 microM respectively. Since incubation conditions have been shown to modulate glucuronidation rates, AZT glucuronidation was performed in various physiological and nonphysiological buffer systems, namely Tris, phosphate, sulfate, carbonate, acetate, human plasma, deproteinized human liver cytosol, and Williams E medium. The data showed that carbonate and Williams E medium, more physiologically relevant buffers, yielded the highest rates of AZT glucuronidation. Km observed in HLM/carbonate was 240 microM closer to that found in hepatocytes, suggesting that matrix differences might cause the kinetic differences observed between liver preparations. Caution should be exercised when extrapolating metabolic lability via glucuronidation or inhibition of UGT enzymes from human liver microsomes, since this system appears to underpredict the degree of lability or inhibition, respectively, due in part to an apparent decrease in substrate affinity.
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Affiliation(s)
- Juntyma J Engtrakul
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer Global Research and Development, Groton, CT 06340, USA
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47
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Gupta RP, He YA, Patrick KS, Halpert JR, Bell NH. CYP3A4 is a vitamin D-24- and 25-hydroxylase: analysis of structure function by site-directed mutagenesis. J Clin Endocrinol Metab 2005; 90:1210-9. [PMID: 15546903 DOI: 10.1210/jc.2004-0966] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Studies were performed to identify the microsomal enzyme that 24-hydroxylates vitamin D, whether 25-hydroxylation occurs, and structure function of the enzyme. Sixteen hepatic recombinant microsomal cytochrome P450 enzymes expressed in baculovirus-infected insect cells were screened for 24-hydroxylase activity. CYP3A4, a vitamin D-25-hydroxylase, and CYP1A1 had the highest 24-hydroxylase activity with 1 alpha-hydroxyvitamin D(2) (1 alpha OHD(2)) as substrate. The ratio of rates of 24-hydroxylation of 1 alpha-hydroxyvitamin D(3) (1 alpha OHD(3)), 1 alpha OHD(2), and vitamin D(2) by CYP3A4 was 3.6/2.8/1.0. Structures of 24-hydroxyvitamin D(2), 1,24(S)-dihydroxyvitamin D(2), and 1,24-dihydroxyvitamin D(3) were confirmed by HPLC and gas chromatography retention time and mass spectroscopy. In characterized human liver microsomes, 24-hydroxylation of 1 alpha OHD(2) by CYP3A4 correlated significantly with 6 beta-hydroxylation of testosterone, a marker of CYP3A4 activity. 24-Hydroxylase activity in recombinant CYP3A4 and pooled human liver microsomes showed dose-dependent inhibition by ketoconazole, troleandomycin, alpha-naphthoflavone, and isoniazid, known inhibitors of CYP3A4. Rates of 24- and 25-hydroxylation of 1 alpha OHD(2) and 1 alpha OHD(3) were determined in recombinant wild-type CYP3A4 and site-directed mutants and naturally occurring variants expressed in Escherichia coli. Substitution of residues showed the most prominent alterations of function at residues 119, 120, 301, 305, and 479. Thus, CYP3A4 is both a 24- and 25-hydroxylase for vitamin D(2), 1 alpha OHD(2), and 1 alpha OHD(3).
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Affiliation(s)
- Ram P Gupta
- Department of Medicine, Medical University of South Carolina, P.O. Box 250775, Charleston, South Carolina 29425, USA
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48
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Emoto C, Murase S, Sawada Y, Iwasaki K. In Vitro Inhibitory Effect of 1-Aminobenzotriazole on Drug Oxidations in Human Liver Microsomes: a Comparison with SKF-525A. Drug Metab Pharmacokinet 2005; 20:351-7. [PMID: 16272753 DOI: 10.2133/dmpk.20.351] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1-Aminobenzotriazole (ABT) is extensively used as a non-specific cytochrome P450 (CYP) inhibitor. In this study, the inhibitory effect of ABT on CYP-dependent drug oxidations was investigated in human liver microsomes (HLM) and compared with that of SKF-525A, another non-specific inhibitor. The following probe activities for human CYP isoforms were determined using pooled HLM: phenacetin O-deethylation (CYP1A2); diclofenac 4'-hydroxylation (CYP2C9); S-mephenytoin 4'-hydroxylation, (CYP2C19); bufuralol 1'-hydroxylation (CYP2D6); chlorzoxazone 6-hydroxylation (CYP2E1); midazolam 1'-hydroxylation, nifedipine oxidation, and testosterone 6beta-hydroxylation (CYP3A). ABT had the strongest inhibitory effect on the CYP3A-dependent drug oxidations and the weakest effect on the diclofenac 4'-hydroxylation. SKF-525A potently inhibited the bufuralol 1'-hydroxylation, but weakly inhibited chlorzoxazone 6-hydroxylation. The inhibitory effects of ABT and SKF-525A were increased by preincubation in some probe reactions, and this preincubation effect was greater in ABT than in SKF-525A. The remarkable IC50 shift (> 10 times) by preincubation with ABT was observed on the phenacetin O-deethylation, chlorzoxazone 6-hydroxylation, and midazolam 1'-hydroxylation. In conclusion, ABT and SKF-525A had a wide range of IC50 values in inhibiting the drug oxidations by HLM with and without preincubation.
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Affiliation(s)
- Chie Emoto
- Department of Pharmacokinetics Dynamics Metabolism, Nagoya Laboratories, Pfizer Japan Inc., Taketoyo, Aichi, Japan
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49
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Baas BJ, Denisov IG, Sligar SG. Homotropic cooperativity of monomeric cytochrome P450 3A4 in a nanoscale native bilayer environment. Arch Biochem Biophys 2004; 430:218-28. [PMID: 15369821 DOI: 10.1016/j.abb.2004.07.003] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Revised: 06/29/2004] [Indexed: 11/28/2022]
Abstract
Mechanistic studies of mammalian cytochrome P450s are often obscured by the phase heterogeneity of solubilized preparations of membrane enzymes. The various protein-protein aggregation states of microsomes, detergent solubilized cytochrome or a family of aqueous multimeric complexes can effect measured substrate binding events as well as subsequent steps in the reaction cycle. In addition, these P450 monooxygenases are normally found in a membrane environment and the bilayer composition and dynamics can also effect these catalytic steps. Here, we describe the structural and functional characterization of a homogeneous monomeric population of cytochrome P450 3A4 (CYP 3A4) in a soluble nanoscale membrane bilayer, or Nanodisc [Nano Lett. 2 (2002) 853]. Cytochrome P450 3A4:Nanodisc assemblies were formed and purified to yield a 1:1 ratio of CYP 3A4 to Nanodisc. Solution small angle X-ray scattering was used to structurally characterize this monomeric CYP 3A4 in the membrane bilayer. The purified CYP 3A4:Nanodiscs showed a heretofore undescribed high level of homotropic cooperativity in the binding of testosterone. Soluble CYP 3A4:Nanodisc retains its known function and shows prototypic hydroxylation of testosterone when driven by hydrogen peroxide. This represents the first functional characterization of a true monomeric preparation of cytochrome P450 monooxygenase in a phospholipid bilayer and elucidates new properties of the monomeric form.
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Affiliation(s)
- Bradley J Baas
- Department of Biochemistry, University of Illinois Urbana-Champaign, 505 South Goodwin Avenue, IL 61801, USA
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Paine MF, Criss AB, Watkins PB. Two major grapefruit juice components differ in intestinal CYP3A4 inhibition kinetic and binding properties. Drug Metab Dispos 2004; 32:1146-53. [PMID: 15269184 DOI: 10.1124/dmd.104.000547] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bergamottin (BG) and 6',7'-dihydroxybergamottin (DHB) are the most abundant furanocoumarins present in grapefruit juice and have been proposed as major intestinal CYP3A4 inhibitors contributing to grapefruit juice-drug interactions. The relative contribution of BG versus DHB to the interaction potential is unclear, in part due to inconsistencies in the literature regarding inhibitory potency. To resolve these inconsistencies, the inhibitory kinetics of each furanocoumarin toward CYP3A4 catalytic activity were systematically characterized using representative probes from two distinct CYP3A4 substrate subgroups (testosterone and midazolam). With human intestinal microsomes, DHB was a substrate-independent reversible (Ki, approximately 0.8 microM) and mechanism-based (KI, approximately 3 microM; kinact, 0.3-0.4 min(-1)) inhibitor of CYP3A4. In contrast, BG was a substrate-dependent reversible inhibitor, with a Ki (13 microM) using midazolam that was 8-fold greater than that using testosterone, but a substrate-independent mechanism-based inhibitor (KI, approximately 25 microM; kinact, approximately 0.35 min(-1)). Similar trends resulted with cDNA-expressed CYP3A4, only the KI values for BG were approximately 10-fold lower than with microsomes. This seemed to reflect a much greater degree of microsomal protein binding by BG compared with DHB. Differential inhibition kinetics and binding properties between BG and DHB could account in part for the apparent in vitro inconsistencies in the literature. Results also emphasize the importance of appropriate substrate selection when designing inhibition studies involving dietary constituents.
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Affiliation(s)
- Mary F Paine
- General Clinical Research Center, Room 3005 Bldg. APCF, CB# 7600, UNC Hospitals, Chapel Hill, NC 27599-7600, USA.
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